R: List classes with assay data listed by chromosome
BeadStudioSetList-class
R Documentation
List classes with assay data listed by chromosome
Description
Container for log R ratios and B allele frequencies stored by chromosome.
Slots
assayDataList:
Object of class "AssayData" ~~
phenoData:
Object of class "AnnotatedDataFrame" ~~
featureDataList:
Object of class "list" ~~
chromosome:
Object of class "integer" ~~
annotation:
Object of class "character" ~~
genome:
Object of class "character" indicating
the genome build. Valid entries are "hg18" and "hg19".
Methods defined for the class
clone2(object, id, prefix="",...)
Performs a deep copy of the ff objects in the assay data elements
of object. A new object of the same class will be
instantiated. The ff objects in the instantiated object will point to
ff files on disk with prefix given by the argument prefix.
A use-case for such a function is that one may want to perform wave
correction on the log R ratios in object, but keep a copy of
the original unadjusted log R ratios. If object is not copied
using clone2 prior to wave correction, the log R ratios will be
updated on disk and the original, unadjusted log R ratios will no
longer be available.
Accessors
baf(object)An accessor for the B allele frequencies
(BAFs). The accessor returns a list where each element of the list is
a matrix of the BAFs for the corresponding element in the SetList
object. While the BAFs have a range [0, 1], they are often saved
internally as integers by multiplying the original BAFs by 1000.
Users can restore the original scale by dividing by 1000.
lrr(object) An accessor for the log R ratios, an
estimate of the copy number (presumably relative to diploid copy
number) at each marker on a SNP array. The accessor returns a list
where each element of the list is a matrix of the log R ratios for the
corresponding element in the SetList object. The log R ratios are
often saved internally as integers by multiplying the original LRRs by
100 in order to reduce the memory footprint of large studies. Users
can restore the original scale by dividing by 100.
Author(s)
R. Scharpf
See Also
See supporting packages for methods defined for the class.